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- PDB-5xsm: Crystal Structure of Transketolase in complex with TPP intermedia... -

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Basic information

Entry
Database: PDB / ID: 5xsm
TitleCrystal Structure of Transketolase in complex with TPP intermediate IV from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


purine nucleotide metabolic process / transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8EO / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Lyu, S.Y. / Hsu, L.J. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L.
History
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8406
Polymers75,0541
Non-polymers7865
Water14,412800
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,68012
Polymers150,1092
Non-polymers1,57210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10450 Å2
ΔGint-57 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.946, 184.259, 98.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-817-

HOH

21A-869-

HOH

31A-1183-

HOH

41A-1462-

HOH

51A-1525-

HOH

61A-1554-

HOH

71A-1590-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 75054.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-8EO / 2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2,5-dihydro-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate


Mass: 427.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N4O7P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 800 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.7 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.97→30 Å / Num. obs: 537705 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.6
Reflection shellResolution: 0.97→1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 0.97→27.893 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.26
RfactorNum. reflection% reflection
Rfree0.1462 26874 5 %
Rwork0.138 --
obs0.1384 537620 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.97→27.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 48 800 5978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085323
X-RAY DIFFRACTIONf_angle_d1.2087244
X-RAY DIFFRACTIONf_dihedral_angle_d6.5363092
X-RAY DIFFRACTIONf_chiral_restr0.113811
X-RAY DIFFRACTIONf_plane_restr0.009938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9684-0.97940.19348140.189115677X-RAY DIFFRACTION92
0.9794-0.99090.19458930.178916943X-RAY DIFFRACTION100
0.9909-1.0030.17019120.16816934X-RAY DIFFRACTION100
1.003-1.01570.17659650.156816920X-RAY DIFFRACTION100
1.0157-1.02910.1618860.149217033X-RAY DIFFRACTION100
1.0291-1.04320.15769400.144116895X-RAY DIFFRACTION100
1.0432-1.05810.14488950.13316998X-RAY DIFFRACTION100
1.0581-1.07390.13359190.122917015X-RAY DIFFRACTION100
1.0739-1.09070.12459130.11416962X-RAY DIFFRACTION100
1.0907-1.10850.12328730.110417064X-RAY DIFFRACTION100
1.1085-1.12770.11339180.105716992X-RAY DIFFRACTION100
1.1277-1.14820.11359320.101716984X-RAY DIFFRACTION100
1.1482-1.17020.11488570.099217011X-RAY DIFFRACTION100
1.1702-1.19410.11028790.097417086X-RAY DIFFRACTION100
1.1941-1.22010.10599550.098916984X-RAY DIFFRACTION100
1.2201-1.24850.11319090.097717009X-RAY DIFFRACTION100
1.2485-1.27970.11379080.099316997X-RAY DIFFRACTION100
1.2797-1.31430.1178420.102517113X-RAY DIFFRACTION100
1.3143-1.3530.11428510.104817136X-RAY DIFFRACTION100
1.353-1.39660.13028460.109117124X-RAY DIFFRACTION100
1.3966-1.44660.12118490.110717080X-RAY DIFFRACTION100
1.4466-1.50450.13148870.111717147X-RAY DIFFRACTION100
1.5045-1.57290.13268380.11317159X-RAY DIFFRACTION100
1.5729-1.65590.12329460.11917061X-RAY DIFFRACTION100
1.6559-1.75960.13628580.131217173X-RAY DIFFRACTION100
1.7596-1.89540.14988980.145917177X-RAY DIFFRACTION100
1.8954-2.08610.15319560.151517134X-RAY DIFFRACTION100
2.0861-2.38780.16089410.159617225X-RAY DIFFRACTION100
2.3878-3.00780.16958740.172917387X-RAY DIFFRACTION100
3.0078-27.90420.17179200.163717326X-RAY DIFFRACTION98

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